RetrogeneDB ID: retro_ocun_418

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:7198307..7198763(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NME2
• Ensembl ID: ENSOCUG00000024946
• Aliases: None
• Description: NME/NM23 nucleoside diphosphate kinase 2 (NME2), mRNA [Source:RefSeq mRNA;Acc:NM_001204750]

Sequence

>retro_ocun_418
ATGGCCCACCTGGAGTGCACTTTCATCACCATCAAGCTGGACAGCGTGCAGCGCGGCCTGGTGGGAGAAATCATCAAGCG
CTTTGAGCAGAAGGGATTCCGCCTGGTGGCCATGTAGTTCCTTCAGGCCTCCAAGGAGCACCTGAAGCAACACTACATGG
ACCTGAAAGACCGCCCGTTCTTCCCGGGGCTGGTGAAGTACATGAACTTGGGGCCGGTCGTGGCCATGGTCTGGGAGGGG
CTGAACGTGGTGAAGACAGGTCGAGTATTGCTCGGGGAGACCGACCCTGCGGACTCTAAGCCGGGCACCATCCACGGGGA
CTTCTGCATCCGGGTTGGCAGGAACATCACTCATGGCAGCAACTCAGTGAAAAGTGCTGAAAAAGAAATAAGCCTGTGGT
TCCAGCCTGAAGAACTGGTCGACTACAAGTCTTGTGCTCACGACTGGGTCTGTGAG

Alignment

ORF - retro_ocun_418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAHLERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQHYIDLKDRPFFPGLVKYMNS
          MAHLE.TFI.IK.D.VQRGLVGEIIKRFEQKGFRLVAM.FL.AS.EHLKQHY.DLKDRPFFPGLVKYMN.
Retrocopy MAHLECTFITIKLDSVQRGLVGEIIKRFEQKGFRLVAM*FLQASKEHLKQHYMDLKDRPFFPGLVKYMNL

Parental  GPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVKSAEKEISLWFQPEELV
          GPVVAMVWEGLNVVKTGRV.LGET.PADSKPGTI.GDFCI.VGRNI.HGS.SVKSAEKEISLWFQPEELV
Retrocopy GPVVAMVWEGLNVVKTGRVLLGETDPADSKPGTIHGDFCIRVGRNITHGSNSVKSAEKEISLWFQPEELV

Parental  DYKSCAHDWVYE
          DYKSCAHDWV.E
Retrocopy DYKSCAHDWVCE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.11 RPM	68.88 RPM
SRP017611_kidney	0.10 RPM	172.71 RPM
SRP017611_liver	0.00 RPM	46.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_418 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_418 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728,
Oryctolagus cuniculus	ENSOCUG00000024946	1 retrocopy	retro_ocun_418 ,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sarcophilus harrisii	ENSSHAG00000014470	3 retrocopies	retro_shar_130, retro_shar_554, retro_shar_781,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,